Re: [PyMOL] dump_binary and PyMOL 1.8 PSE files

[Thomas H. <tho...@sc...>]

Hi Bob,

I assume those are PSE files with setting "pse_binary_dump=on". This is not the default. You can load such files into PyMOL, set pse_binary_dump=off and save it as a regular serialized PSE. I definitely recommend the conversion step over reimplementing the "pse_binary_dump" decoding. Right now there are 3 binary atom layouts (for 1.7.6, 1.8.0 and 1.8.2). Grep the PyMOL code for "AtomInfoTypeConverter" if you're interested in the details.

The default (in 1.8.2) is to save PyMOL 1.7.6 compatible PSE files, and with the "pse_export_version" setting you can also export for older PyMOL versions.

Cheers,
  Thomas

On 08 Aug 2016, at 07:57, Robert Hanson <ha...@st...> wrote:

> Thomas,
> 
> In reading PyMOL PSE files into Jmol I have recently run into the problem with some of these files (version 1.8.2.3). Jmol has no problem reading the standard Pickle format, but there seems to be an option in PyMOL to serialize binary data structures as BINSTRING or SHORT_BINSTRING format along with other standard strings. This sounds like a great idea; I have no doubt that this will lead to considerably smaller PSE files and also faster loading. However, I'm struggling with atom information deserialization. 
> 
> Q: Is this the default format now for saving PyMOL PSE files?
> 
> Q: Is there a way to turn that off? 
> 
> Q: In order to do this properly, how many versions of the atom info data structure do I need to be able to process? 
> 
> Bob
> 
> -- 
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
> 
> 
> If nature does not answer first what we want,
> it is better to take what answer we get. 
> 
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.